It's not entirely on topic but I'm going to suggest you seriously consider adopting GNU/Linux as your development platform of choice. It's a toolchain hacker's dream, documentation on the tools is generally at hand, and it uses openly-sourced tools for pretty much everything so you can either read the source to see how they work or read the detailed specificaction to see what they're supposed to do.
You'll find MinGW is a reduced copy of the GNU environment you usually get by default on Linux, so you're probably already familiar with much of how things work. You can also bring much of what you learn back to MinGW to apply to Windows applications.
Trust me, you're going to make the switch sooner or later.
Linux uses the Extensible Link Format (ELF) for its binary objects (object files, shared libraries, executable binaries). If you learn and understand the basics of that, it will go a long way toward understanding what you would need to do to convert other binary formats (.bin, COFF, etc).